Monday, June 14, 2010

Did MicroRNAs Shape the Cambrian Explosion?

The fossil record reveals a history of life characterized by the abrupt appearance of new species followed by no change and eventual extinction in most cases. Needless to say, abrupt appearances and no change is not exactly what evolution expected. Much of this was known in Darwin's time and he figured that the fossil record was incomplete. Today such speculation doesn't work anymore. The evidence reveals even more clearly this pattern of abrupt appearances followed by stasis. As one recent paper explained:

Beginning some 555 million years ago the Earth’s biota changed in profound and fundamental ways, going from an essentially static system billions of years in existence to the one we find today, a dynamic and awesomely complex system whose origin seems to defy explanation. Part of the intrigue with the Cambrian explosion is that numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time.

As in Darwin's day, the fossil record does not match evolutionary expectations and evolutionists have been trying to solve the riddle. How can the empirical scientific data be explained by evolution? One new idea is to have the recently discovered microRNAs do the heavy lifting.

MicroRNAs are short snippets of DNA, about 20 nucleotides long, that help regulate protein production. The idea is that:

miRNAs might be instrumental in canalizing development such that phenotypic variation decreases through geologic time at the cost of increasing developmental precision, allowing for subsequent increases in morphological complexity.

The big words hide the fact that there is no substance to the proposal. Here is the proposal in English (my translation):

New forms abruptly appeared because evolution somehow created them. In fact, there was an abundance of these new forms, representing dozens of different designs, and many variations on each design. As luck would have it, evolution began creating microRNAs which suppressed much of that variation because, after all, microRNAs regulate protein production. So microRNAs explain the reductions in variation that follow the explosions. And, oh by the way, microRNAs also helped evolution create new wonders, not that it couldn't already, but you know, they helped.

This is the usual just-add-water view of science that prevails courtesy of evolution. Incredibly complex organisms which defy our understanding just appear now and then. They might give rise to more incredible creations, or maybe not. Meanwhile, the details of what actually happened remain a complete mystery.

For instance, the notion that microRNAs just began to proliferate on their own is absurd. They are one part of a mind-boggling regulation network. Indeed, the microRNAs themselves (which regulate protein production remember) are regulated by proteins. As new research is gradually elucidating, "MicroRNAs control the translation of mRNAs into proteins, and proteins in turn regulate the microRNAs at various levels.”

Not only is the production of microRNAs tightly controlled, but they are carefully removed from action as well, as a consequence of "a dense network of regulatory mechanisms."

But for a moment let's set all the problems aside. Let's give evolution every break and consider that this fanciful story may really be not the creation myth it appears to be, but the real thing. Taking this narrative at face value, it would mean that evolution produced the elaborate mechanisms and machinery (and sequences) of microRNAs, so that evolution then could really take off. It would be the ultimate Rube Goldberg device. Evolutionists, who are not the least abashed at presenting such tripe, are seriously telling each other that evolution created evolution. This is truly astonishing.

With each new failed expectation and each new unfounded absurd speculation, evolutionists are digging themselves deeper and deeper in their hole. Religion drives science, and it matters.

24 comments:

I was going to respond to this with specific objections to what you've written, Cornelius, but I'm just not sure it's worth it. If you think that evolutionary biologists legitimately searching for possible mechanisms behind evolutionary change constitutes a "just-add-water view of science", then your view of the scientific process is so warped that I don't think it's possible to change your mind through rational discussion.

Putting aside the obvious rhetoric contained within the phrase, what would you suggest, Cornelius, as an alternative to a "just-add-water view of science"? I'm quite interested.

OK, so you have decided not to respond because you think that Dr. Hunter is beyond help. But what about the rest of us who would benefit from your superior knowledge and your flawless presentation style. C'mon go ahead and dazzle us. Show us where and why Dr. Hunter is hopelessly outclassed by the exceptionally high quality evolutionary arguments. We will be waiting...and waiting

Cornelius practices the time-tested technique known as the Gish Gallop in certain circles. People with expertise in relevant fields have tried to engage Cornelius at some length on various subjects, but he doesn't seem interested in that sort of dialog.

Here is my latest attempt on the supposed incompatibility of evolution and thermodynamics for example.

The fossil record reveals a history of life characterized by the abrupt appearance of new species followed by no change and eventual extinction in most cases.

WHAT?!!?!

I don't know whether to laugh or cry. You really think that is the pattern the fossil record shows? You couldn't be more wrong. Let's just take another snippet of your post to illustrate why...

Part of the intrigue with the Cambrian explosion is that numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye

Technically true, but oh so misleading. Take a look at this picture here:

http://paleobiology.si.edu/burgess/pikaia.html

This simple worm called Pikaia, found in the Cambrian Explosion is widely believed to be the SINGLE REPRESENTATIVE of the whole cordata phylum. In other words, all vertibrates - fish, amphibians, reptiles, birds and mammals - all find a representative in the Cambrian Explosion in this single creature.

You simply cannot reconcile the idea that a huge number of animal phyla have fossilized representatives from the Cambrian period with the idea that animals do not diversify.

It is not the case that we find numerous species of fish, numerous species of amphibians, numerous species of reptiles, birds and mammals, etc, in the Cambrian period and the number of species get FEWER over time. That would be good evidence for what you are saying. Fish, amphibians, reptiles, birds and mammals all have ancestors in the Cambrian period - THE SAME ONES!!

It is only through time and evolution that these creatures diversify and initially tiny differences become vast phylum-wide characteristics. A far, far cry from your grotesque characature of the history of life the fossil record reveals.

It appears to be a 'chicken and egg' problem. The only answer is God did it.

Shhh, you're not supposed to say the 'G' word... You're supposed to pretend it's some OTHER omnipotent, supernatural being with miraculous powers who is completely anonymous. That way ID doesn't *quite* so blatantly resemble Creationism.

===I was going to respond to this with specific objections to what you've written, Cornelius, but I'm just not sure it's worth it.===

Evolutionists insist their idea is an undeniable fact and their explanations of how it actually is supposed to have occurred are just-so stories. When you point this out the evolutionist responds with the old "well you just don't know what you're talking about ..."

===If you think that evolutionary biologists legitimately searching for possible mechanisms behind evolutionary change constitutes a "just-add-water view of science", then your view of the scientific process is so warped that I don't think it's possible to change your mind through rational discussion. ===

Evolutionists claim their problematic idea is an undeniable fact based on metaphysical claims, and I'm the one with the warped view of science.

===Putting aside the obvious rhetoric contained within the phrase, what would you suggest, Cornelius, as an alternative to a "just-add-water view of science"? I'm quite interested. ===

And there is the protectionist contrastive thinking that is at the core of evolutionary thought. Insist an absurd idea is a fact, and then with self-righteous indignation protect it by requiring skeptics to solve the problem. If evolutionists are looking for a warped view of science, they should look closer to home.

Dr. Hunter is absolutely right, Darwinian worshippers are groping to keep their myth alive. Darwinists are like a rabid religious cult when their creation myth is exposed, they bite back with the irrational refrain “what would you suggest”, as if the popularity of other alternatives could justify their irrationalism. When a myth is as bankrupt as Darwinism even one of its Darwinian Priors have to admit that NS+RM is incapable of explaining how new forms were created, he decided that it was time to give the con game a new face lift and call it evo devo.

Unfortunately for these Darwinian troglobytes couldn’t see is that the further back they dig the more complex it is and the more the evidence shows of design. Why were these regulatory gene created? How were they created? How did the pathway of these miRNA formed? What good is shining a light on a Darwinian troglobyte but they don’t have eyes to see.

"Indeed, the microRNAs themselves (which regulate protein production remember) are regulated by proteins."

RNAs are all regulated, in all cells. After all, a cell can't have a messenger RNA or defective tRNAs sitting around for all time. Regulation and the demand to recycle nucleotides dictates this.

Dr. Hunter proposes microRNAs and a specific new regulatory machinery arose simultaneously. That sounds silly, and is quite a hurdle. But it appears microRNA regulation and other (mRNA) regulation share key proteins.

In this case, when novel microRNAs evolved, they could be funneled into the existing (and ancient) RNA regulation machinery. Evolution could then fine-tune regulatory functions over vast time.

But, in classic Dr. Hunter fashion, he ignores what is actually know about RNA regulation in general:

XRN-2 is an exonuclease and the subject of the referenced paper. It is highly conserved all the way down to yeast (and related activities are found in bacteria). It has been shown to also help degrade defective tRNAs, works on rRNAs, and exist in P-granules, where it degrades mRNAs.

So, we've got a general regulator of RNAs that has been adapted to microRNA regulation. Not even a chicken or the egg problem. Pre-existing RNA regulation. New class of RNA. Diversification and specification of regulation. Evolution.

Sounds so much less silly when you present the facts and the actual proposals.

"In this case, when novel microRNAs evolved, they could be funneled into the existing (and ancient) RNA regulation machinery. Evolution could then fine-tune regulatory functions over vast time."

Can you even postulate a mechanism for your proposed funneling process?

By now you should expect this mechanism question from me since that is the obvious problem with a just so story. In fact it is good scientific thinking to consider a probable mechanism before blabbing about a new episode "Wish come true". (I honestly hope to be proven wrong.)

It is far more productive to accept design and continue the obvious "reverse engineering" to solve real life problems.

"Can you even postulate a mechanism for your proposed funneling process?"

I already did. Non-specific endonucleases degrade RNAs. MicroRNAs evolve, and are subject at first to general degradation based on their content and structure. The general degradation machinery then diverges and specifies as a micro-RNA regulatory pathway. The conservation and intersection of the modern pathways suggests this.

"It is far more productive to accept design and continue the obvious "reverse engineering" to solve real life problems."

Right. And what medical advance has ID brought us? How can we hope to understand the workings of a system is we don't understand its origins, its constraints in evolution, its shortcomings? How can we test hypotheses if we ignore common descent, and reject model organisms, homology and deep homology? As one of your comrades pointed out, it is 'stupid' to predict the designer has human genes and processes functioning in plants, yeast, and worms. Maybe you should go a few threads back and argue this point with him.

By now you should expect this mechanism question from me since that is the obvious problem with a just so story. In fact it is good scientific thinking to consider a probable mechanism before blabbing about a new episode "Wish come true". (I honestly hope to be proven wrong.)

Speaking of incoherent babbling Michael, when can we expect you to provide a description of those ID mechanisms? I've only been asking you ever since I got here, and you've cowardly slunk away every time.

You don't even have a 'just-so-story' for your IDC fantasy, just bluster and hot air. You've got a whole lotta nothin'.

As I mentioned in my first post, general degradation machinery is the exonucleases found in all living organisms.

Besides that you believe that evolution is impossible, I'm not sure what warranted the LOL.

I've presented a working hypothesis for the evolution of microRNAs and their regulation that does not require both to arise at the same time, in their modern form. This is supported by the intersection of the microRNA specific, and RNA general degradation pathways. In light of this, Dr. Hunters critique falls short.

But I'm tired of always being on the hotseat.

Care to answer the second half of my post?

"Right. And what medical advance has ID brought us? How can we hope to understand the workings of a system is we don't understand its origins, its constraints in evolution, its shortcomings? How can we test hypotheses if we ignore common descent, and reject model organisms, homology and deep homology? As one of your comrades pointed out, it is 'stupid' to predict the designer has human genes and processes functioning in plants, yeast, and worms. Maybe you should go a few threads back and argue this point with him.

BTW, wanna tell me in what organism miRNAs were discovered?

What design inference led to their recognition in humans?"

How did you detect the microRNA pathway is designed? By what mechanism?

RobertC XRN-2 is an exonuclease and the subject of the referenced paper. It is highly conserved all the way down to yeast (and related activities are found in bacteria). It has been shown to also help degrade defective tRNAs, works on rRNAs, and exist in P-granules, where it degrades mRNAs.

Can you please provide reference data to support your claim XRN2 is used to degrade mRNAs?

RobertC I already did. Non-specific endonucleases degrade RNAs. MicroRNAs evolve, and are subject at first to general degradation based on their content and structure. The general degradation machinery then diverges and specifies as a micro-RNA regulatory pathway. The conservation and intersection of the modern pathways suggests this.

Michael is right. This is complete gibberish. This doesn’t even rise to the level of just so stories. You either have to be delusional or sinisterly deceptive to push this kind of explanation as science. 1. A non-specific endonuclease gene just pop into the DNA at the right place. 2. The signal proteins required to activate that regulatory gene just happen to pop in at the same time. 3. The endonuclease gene for some strange reason doesn’t transcribe into a mature miRNA but magically turns into this pre-miRNA with funky looking loops. 4. The magic continues with Peter Pan flying in with the Dicer enzyme to clip these loops off. 5. Poof, a miRNA is born. This is a rough sketch of just how fairytales begin in the Magic Kingdom of Darwinian evolution. And soon you will have more magic to create other little baby miRNAs, then comes an explosion of phyla, before you know it your talking and walking ape mommy gives birth to you. All this is possible when you wish upon the Darwinian star.

Any literate person realizes I said none of those things. That your side requires such sinister parody to even have a shred of an argument is telling. You can't fight with science, so you create your own silly version of it. Whatever makes you feel good, but don't expect to win very many followers with such ugly deceit.

The way you've constructed the parody is a bit off. I think you've learned a few key terms, but maybe you should continue your education.You might start here:

My original point was the notion that microRNAs and basic RNA regulatory machinery would have to simultaneously co-evolve is silly, because generic RNA regulatory mechanisms (and probably RNAseIII would have pre-existed. These mechanisms then diversified and specified.

You also seem to mistake a functional hypothesis for the evidence this is definitively the case. However, a hypothesis allows for science to proceed, while you think these are 'stupid' things as you've clearly stated before.

RobertC My original point was the notion that microRNAs and basic RNA regulatory machinery would have to simultaneously co-evolve is silly

Really, let’s look at what you said.”So, we've got a general regulator of RNAs that has been adapted to microRNA regulation. Not even a chicken or the egg problem. Pre-existing RNA regulation. New class of RNA. Diversification and specification of regulation. Evolution.”

You said this is not a “chicken or the egg problem” that means there is no dependency, like they do now, between which one get created first, that must mean they were magically created at the same time. The only difference is that instead of using the word abracadabra, you use words like adapted. They are both equally vacuous.

RobertC You also seem to mistake a functional hypothesis for the evidence

Except I was not the one who said this, ”But, in classic Dr. Hunter fashion, he ignores what is actually know about RNA regulation in general”. You didn’t seem to think that it was a hypothesis when you made that statement did you? Because you also said, ”How can we hope to understand the workings of a system is we don't understand its origins”, and we know nothing about how miRNA came about nor any of its pathways. So are you saying Dr. Hunter was right to what we actually know about RNA regulation, which is nothing.

"chicken or the egg problem” that means there is no dependency, like they do now, between which one get created first, that must mean they were magically created at the same time."

No. Quite the opposite. The chicken and the egg is a causality dilemma where the consequence of the phenomenon is claimed to be its root cause. In this case, we have evidence from phylogeny that RNAses and the regulation of RNA predates microRNA. So the causality dilemma is implied, but unevidenced, and most likely false. Similarly, the dilemma of two processes arising simultaneously has been insinuated by Dr. Hunter, for no defensible reason.

”But, in classic Dr. Hunter fashion, he ignores what is actually know about RNA regulation in general”. You didn’t seem to think that it was a hypothesis when you made that statement did you?"

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/